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- PDB-8gdw: Crystal structure of Domain Related to Iron (DRI) from cyanobacteria -

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Basic information

Entry
Database: PDB / ID: 8gdw
TitleCrystal structure of Domain Related to Iron (DRI) from cyanobacteria
ComponentsSsr1698 protein
KeywordsMETAL BINDING PROTEIN / Heme binding protein / DUF2470 / heme homeostasis / succinate dehydrogenase / zinc and heme binding sites
Function / homologyDomain of unknown function DUF2470 / Domain of unknown function (DUF2470) / Haem oxygenase HugZ-like superfamily / Ssr1698 protein
Function and homology information
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsKumaran, D. / Grosjean, N. / Blaby, E.C.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)Quantitative Plant Science Initiative SFA United States
CitationJournal: Nat Commun / Year: 2024
Title: A hemoprotein with a zinc-mirror heme site ties heme availability to carbon metabolism in cyanobacteria.
Authors: Grosjean, N. / Yee, E.F. / Kumaran, D. / Chopra, K. / Abernathy, M. / Biswas, S. / Byrnes, J. / Kreitler, D.F. / Cheng, J.F. / Ghosh, A. / Almo, S.C. / Iwai, M. / Niyogi, K.K. / Pakrasi, H.B. ...Authors: Grosjean, N. / Yee, E.F. / Kumaran, D. / Chopra, K. / Abernathy, M. / Biswas, S. / Byrnes, J. / Kreitler, D.F. / Cheng, J.F. / Ghosh, A. / Almo, S.C. / Iwai, M. / Niyogi, K.K. / Pakrasi, H.B. / Sarangi, R. / van Dam, H. / Yang, L. / Blaby, I.K. / Blaby-Haas, C.E.
History
DepositionMar 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Ssr1698 protein
BBB: Ssr1698 protein
CCC: Ssr1698 protein
DDD: Ssr1698 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4898
Polymers45,2274
Non-polymers2624
Water61334
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.716, 87.230, 57.241
Angle α, β, γ (deg.)90.000, 94.981, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Ssr1698 protein / Domain Related to Iron / DRI


Mass: 11306.716 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa / Gene: ssr1698 / Production host: Escherichia coli (E. coli) / References: UniProt: P73129
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 25% PEG3350, 100 mM Bis-Tris, pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 15, 2019
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.35→29.5 Å / Num. obs: 20972 / % possible obs: 99 % / Redundancy: 5.3 % / Biso Wilson estimate: 56.6 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.055 / Net I/σ(I): 15
Reflection shellResolution: 2.35→2.41 Å / Redundancy: 5 % / Rmerge(I) obs: 0.736 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1362 / CC1/2: 0.76 / % possible all: 87.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5BNC

5bnc


Resolution: 2.35→29.5 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / SU B: 8.899 / SU ML: 0.203 / Cross valid method: FREE R-VALUE / ESU R: 0.308 / ESU R Free: 0.235
RfactorNum. reflection% reflection
Rfree0.2474 1027 4.901 %
Rwork0.197 19927 -
all0.199 --
obs-20954 98.989 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 61.989 Å2
Baniso -1Baniso -2Baniso -3
1--0.376 Å20 Å22.54 Å2
2---3.183 Å2-0 Å2
3---3.069 Å2
Refinement stepCycle: LAST / Resolution: 2.35→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3096 0 4 34 3134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133140
X-RAY DIFFRACTIONr_bond_other_d0.0030.0162952
X-RAY DIFFRACTIONr_angle_refined_deg1.5451.6384240
X-RAY DIFFRACTIONr_angle_other_deg1.3411.5846824
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6965400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.66725.122164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.94415560
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0561512
X-RAY DIFFRACTIONr_chiral_restr0.0590.2432
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023624
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02656
X-RAY DIFFRACTIONr_nbd_refined0.210.2686
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2030.22654
X-RAY DIFFRACTIONr_nbtor_refined0.1610.21524
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.21564
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.259
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1130.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0850.211
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2240.231
X-RAY DIFFRACTIONr_nbd_other0.240.285
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1480.27
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0110.21
X-RAY DIFFRACTIONr_mcbond_it5.4256.3751612
X-RAY DIFFRACTIONr_mcbond_other5.4276.3741611
X-RAY DIFFRACTIONr_mcangle_it8.1819.5562008
X-RAY DIFFRACTIONr_mcangle_other8.1789.5562009
X-RAY DIFFRACTIONr_scbond_it5.6446.8551528
X-RAY DIFFRACTIONr_scbond_other5.6426.8551529
X-RAY DIFFRACTIONr_scangle_it8.69810.0282232
X-RAY DIFFRACTIONr_scangle_other8.69610.0282233
X-RAY DIFFRACTIONr_lrange_it12.52975.7013332
X-RAY DIFFRACTIONr_lrange_other12.52975.6873331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.410.323750.2991281X-RAY DIFFRACTION87.7
2.411-2.4770.292800.2721474X-RAY DIFFRACTION100
2.477-2.5490.319720.2511371X-RAY DIFFRACTION100
2.549-2.627711352X-RAY DIFFRACTION99.8596
2.627-2.7130.325810.2441333X-RAY DIFFRACTION100
2.713-2.8080.338800.2341243X-RAY DIFFRACTION100
2.808-2.9140.291650.2241245X-RAY DIFFRACTION100
2.914-3.0330.282640.2251173X-RAY DIFFRACTION100
3.033-3.1670.335670.2251147X-RAY DIFFRACTION100
3.167-3.3210.261470.2221077X-RAY DIFFRACTION99.9111
3.321-3.50.275550.2161064X-RAY DIFFRACTION100
3.5-3.7120.28460.205978X-RAY DIFFRACTION99.7079
3.712-3.9670.243440.192924X-RAY DIFFRACTION100
3.967-4.2830.252450.167856X-RAY DIFFRACTION100
4.283-4.6890.179360.151815X-RAY DIFFRACTION100
4.689-5.2380.254220.171731X-RAY DIFFRACTION100
5.238-6.040.2300.195634X-RAY DIFFRACTION100
6.04-7.3770.16525558X-RAY DIFFRACTION99.4881
7.377-1014430X-RAY DIFFRACTION99.3289

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